RNAcentral Sequence Search DevOps code

This repository contains DevOps code for managing the RNAcentral sequence search microservice infrastructure.

Installation

There are 3 environments:

• docker-compose to start up the database, producer, and consumer for local development using docker-compose up.

• local when developing new features, both producer and consumer are supposed to be run from local machine and postgres database server is also meant to be run on localhost:5432

• production this is the production cloud environment, where the code is deployed to openstack

There is also a test environment that is not currently documented. It is used for running unit-tests on local machine only, it is not using any database or network communications.

Manual deployment in production

Requirements

• Terraform

1. Create terraform/providers.tf using the providers.tf.template file.

2. Generate sequence_search_rsa key:

cd terraform && ssh-keygen -t rsa -b 4096

3. Run terraform init && terraform apply to create the infrastructure

Development workflow

1. Choose terraform workspace:

   terraform workspace select <env> where env can be default, test or covid. Once the workspace is selected, terraform will choose the correct tfstate file and will know how to configure ssh keys.

2. Run terraform apply.

   This will check that the infrastructure is up and running, configure ssh keys, and update ansible inventory on each run.

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Additional notes

The installation and configuration of VMs in production is done via Ansible.

How to generate the hosts file used by Ansible

1. Run terraform show -json > current_state

2. Run this python script to create the ansible/hosts file:

python hosts.py

3. You can now run ansible commands with:

pushd ansible; ansible-playbook -i hosts <file>

Restart the sequence search

In case you need to restart the sequence search, run these commands:

ansible-playbook -i hosts producer.yml --tag restart

ansible-playbook -i hosts consumers.yml --tag restart

Frontend

The embedded component is being used as frontend code. It is not needed in production, but it can be useful for testing.

The code is available here: https://github.com/RNAcentral/rnacentral-sequence-search-embed

Using terraform workspaces for blue-green release

1. Choose a workspace: terraform workspace select <env>

Env can be default, test or covid. All subsequent terraform commands will apply only to that environment.

2. Apply terraform changes: terraform apply

The main.tf will automatically configure the correct IP depending on the workspace.

3. Update local ssh config: ansible-playbook -i hosts localhost.yml

The IP address will be set depending on the current terraform.tfstate which is enabled by the terraform workspace.

4. Run any other ansible playbooks: ansible-playbook -i hosts producer.yml

How to create a load balancer and move from one environment to another

1. pushd terraform/load_balancer; terraform apply; popd

2. Run the command bellow passing the IPs as variables on the command line:

   cd ansible_load_balancer
   ansible-playbook -i hosts --private-key=../terraform/load_balancer/load_balancer_rsa --extra-vars "main_ip=main.ip.address fallback_ip=fallback.ip.address" load_balancer.yml
   

The load balancer is an nginx server that proxies http requests to the currently selected producer machine's 8002 port. If you want to change the port of producer machine, go to load_balancer.yml playbook and change the nginx_backend_port variable.

If you want to update nginx configuration, make changes in ansible_load_balancer/roles/ansible_load_balancer/templates/upstream.conf.js.

Manual installation in local environment

1. git clone https://github.com/RNAcentral/rnacentral-sequence-search.git
2. cd rnacentral-sequence-search
3. python3 -m venv ENV
4. source ENV/bin/activate
5. pip3 install -r sequence_search/requirements.txt
6. pushd sequence_search/consumer
7. curl -OL http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz && \ tar -zxvf hmmer-3.2.1.tar.gz && \ cd hmmer-3.2.1 && \ ./configure --prefix /usr/local && \ make && \ make install && \ cd easel; make install && \ cd ../../
8. curl -OL http://eddylab.org/infernal/infernal-1.1.3.tar.gz && \ tar xf infernal-1.1.3.tar.gz && \ cd infernal-1.1.3 && \ ./configure --prefix /usr/local && \ make && \ make install && \ cd ../
9. mkdir rfam && \ cd rfam && \ curl -OL ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz && \ gunzip Rfam.cm.gz && \ cmpress Rfam.cm && \ cd ../
10. git clone https://github.com/nawrockie/cmsearch_tblout_deoverlap.git
11. rsync <database/fasta/files/location/on/local/machine> databases/ - copy .fasta files with databases we want to search against into sequence_search/consumer/databases folder
12. If necessary, update the contents of sequence_search/consumer/rnacentral_database.py accordingly (there's a mapping of database human-readable names to file names).
13. popd
14. pushd sequence_search/producer/static
15. git clone https://github.com/RNAcentral/rnacentral-sequence-search-embed.git && \ cd rnacentral-sequence-search-embed && \ git checkout localhost
16. popd
17. docker build -t local-postgres -f postgres/local.Dockerfile postgres - this will create an image with postgres databases.
18. docker run -d -p 5432:5432 -e POSTGRES_PASSWORD=postgres -t local-postgres - this will create and start an instance of postgres on your local machine's 5432 port.
19. python3 -m sequence_search.db - creates necessary database tables for producer and consumer to run
20. python3 -m sequence_search.producer - starts producer server on port 8002
21. python3 -m sequence_search.consumer - starts consumer server on port 8000
22. brew install memcached - install memcached using Homebrew
23. memcached - start memcached server

Sources of inspiration

• https://cloudbase.it/easily-deploy-a-kubernetes-cluster-on-openstack/ - OpenStack console client commands
• https://docs.oracle.com/cd/E36784_01/html/E54155/clicreatevm.html - example OpenStack provisioning commands
• https://github.com/kubernetes-incubator/kubespray - Kubespray main repo
• https://gist.github.com/yonglai/d4617d6914d5f4eb22e4e5a15c0e9a03 - Ansible gist for installing Docker
• https://tasdikrahman.me/2017/03/19/Organising-tasks-in-roles-using-Ansible/ - plays vs roles vs tasks
• https://github.com/ANXS/postgresql - Ansible postgres role
• https://www.ajg.id.au/2018/05/23/ansible-ssh-jump-hosts-and-multiple-private-keys/ - working with jumphosts
• https://platform9.com/blog/how-to-use-terraform-with-openstack/ - sample Terraform/OpenStack configuration
• https://github.com/diodonfrost/terraform-openstack-examples/tree/master/01-sample-instance - more Terraform examples
• https://heapanalytics.com/blog/engineering/terraform-gotchas - explanation of Terraform configuration
• https://alex.dzyoba.com/blog/terraform-ansible/ - how to generate Ansible inventory from Terraform